Abstract: A software platform for analyzing gene expression, gene annotation, and sample information in a relational format comprises a gene expression module (200) with a data warehouse (210) for storing quantitative gene expression measurements for tissues and cell lines screened using various assays, information on bio-samples (404) and donors, experimental information, and a gene index comprising curated information from external information sources. A connection module (300) permits loading of more than one source of gene expression, gene annotation into the data warehouse (210) so that it may be searched in combination with pre-existing data in the warehouse. A user interface provides for loading user-derived data, initiating searches and for visualizing search results.

Abstract: The present invention pertains to a system and method of analyzing gene expression, gene annotation, and sample information in a relational format supporting efficient exploration and analysis, comprising: providing a data warehouse which comprises a gene expression database for storing quantitative gene expression measurements for tissues and cell lines screened using various assays; a clinical database for storing information on bio-samples and donors; and a fragment index for biological properties for DNA fragments; receiving a query regarding gene expression of one or more DNA fragments; determining the level of gene expression of the one or more DNA fragments; correlating the level of gene expression with the clinical database and the fragment index; and displaying the results of said correlation.

Abstract: Acidic amino acid extensions to multimeric proteins, particularly nucleic acid (e.g., DNA or RNA) binding proteins, provide novel acidically modified proteins which can inhibit the function of cellular proteins, thereby regulating and controlling cell growth. The acidically modified nucleic acid binding proteins are engineered to contain a plurality of acidic amino acids appended to the proteins, generally as extensions of the multimerization or dimerization domain at the amino terminus, and can replace the basic region DNA binding domain of a DNA binding protein. The acidically extended nucleic acid binding proteins act as potent dominant negatives which were demonstrated to inhibit the activation of endogenous transactivators, such as AP1. The invention provides novel methods to create such acidically modified DNA binding proteins which can specifically and stably heterodimerize with cellular regulatory proteins and control cell growth.

Abstract: Acidic amino acid extensions to multimeric proteins, particularly nucleic acid (e.g., DNA or RNA) binding proteins, provide novel acidically modified proteins which can inhibit the function of cellular proteins, thereby regulating and controlling cell growth. The acidically modified nucleic acid binding proteins are engineered to contain a plurality of acidic amino acids appended to the proteins, generally as extensions of the multimerization or dimerization domain at the amino terminus, and can replace the basic region DNA binding domain of a DNA binding protein. The acidically extended nucleic acid binding proteins act as potent dominant negatives which were demonstrated to inhibit the activation of endogenous transactivators, such as AP1. The invention provides novel methods to create such acidically modified DNA binding proteins which can specifically and stably heterodimerize with cellular regulatory proteins and control cell growth.

Abstract: Acidic amino acid extensions to multimeric nucleic acid (e.g., DNA or RNA) binding proteins provide novel nucleic acid binding proteins which can inhibit the function of cellular proteins, thereby regulating and controlling cell growth. The nucleic acid binding proteins are engineered to contain a plurality of acidic amino acids appended to the proteins, generally as extensions of the multimerization or dimerization domain at the amino terminus. The acidically extended nucleic acid binding proteins act as potent dominant negatives which were demonstrated to inhibit the activation of endogenous transactivators, such as AP1. The invention provides novel methods to create DNA binding proteins which can specifically and stably heterodimerize with cellular regulatory proteins and control cell growth. Suitable nucleic acid binding proteins for acidic extensions include members of transcription regulatory protein families, e.g.